The prokaryotic world is divided into the Bacteria and Archaea domains. Although these two groups are evolutionarily and biochemically distinct, both are found in almost every environment investigated. The roles bacteria play in the environment are extensive, covering a range of functions from nutrient cycling to disease progression. Although our understanding of archaeal roles has lagged behind bacterial research, archaea are well-recognized components of many systems, from rumen digestion and the production of greenhouse gases from livestock (23) to microbiologically influenced corrosion and biofouling of industrial water systems and gas pipelines (4).
Because of the genetic distinction between the prokaryotic domains, molecular targeting of microbial populations must be domain-specific. Within the bacterial realm, robust universal polymerase chain reaction (PCR) primer sets have been well-characterized and utilized to target the bacterial 16S rRNA gene and the group I chaperonin (cpn60) gene (1, 18). Both have provided a wealth of data towards understanding the bacterial members of complex communities, with the protein-coding chaperonin gene having advantages in terms of phylogenetic resolution. Universal primers for the amplification of the cpn60 “universal target” sequence are patented (11, 12, 17) and have been widely applied to the detection, identification, quantification and phylogenetic analysis of bacteria and eukaryotes in clinical and environmental samples (2, 3, 6-10, 13-16, 19, 20, 22, 24, 26, 28). Within the archaeal realm, universal PCR primers for the entire domain have remained limited to the archaeal 16S rRNA gene (1). With the continued increase in publicly available archaeal genome sequences, it is now possible to investigate and evaluate non-16S rRNA gene targets as potential universal archaeal markers with improved resolving power over the 16S rRNA gene.